The Captain and Kathryn
by Katy Jane
Summary: Can the Captain and Kathryn learn to live with eachother?
1. Prologue

Disclaimer: Everything trek belongs to Paramount, I am but a lowly fan. But I am soooo not happy with them so they can BITE ME!!!!!!!!!!!!!!!!  
  
  
  
The Captain and Kathryn: Prologue  
  
By: Katy Jane  
  
Today I will perform the ceremony. I should be happy for him, I am happy for him, truly I am. I'm sad for my self; sad because I know that this could have been mine, should have been mine, but I was too stubborn, to blind, too stuck on protocol, to let it happen. I have cried thousands of tears for what I have lost and now my captain's facade is securely in place and I show no hint of my emotions, I may as well be a Vulcan. I take a deep breath and enter the holodeck.  
  
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"Captain." He greets me with a warm smile, but not the same smile he has given me in years past, he reserves that for her now. He doesn't call me Kathryn anymore either, that too only belongs to her.Â  If it had been anyone but her this would have been easier, but it is her, and now I have no choice but to face the fact that it could have been me.  
  
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Â I take my place before the couple, their love so obvious in their eyes, and for a moment I slip and let my pain show in mine. He sees and gives me an apologetic, almost sad look. I don't want his pity, I brought this on myself. I quickly snap my facade back in place and begin.  
  
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Â "We are gathered here today to witness the union of Commander Chakotay andÂ  Kathryn Elizabeth Janeway... 


	2. Chapter One

1 Captain and Kathryn  
  
By Katy Jane  
  
Four months earlier…  
  
Once the away team materialized on the uninhabited M-class planet they separated out into groups and began scanning for edible vegetation. The captain and the commander were side by side as they moved away from the other team members. He glanced over at her; she looked content, maybe even happy. As she scanned with the tricorder in her right hand she idly let her left hand brush lightly over a large white flower.  
  
She was letting her shields down, just slightly and he decided to take advantage of the situation. He plucked one of the blossoms and handed it to her with a full dimpled smile. She took the flower and smiled back. He was flirting with her but she was flirting right back. It was subtle, and to the untrained observer the overtures might have gone unnoticed. Chakotay knew what was going on, The Captain was letting Kathryn come out and play. He wished she would do that more often. The pair continued on their way exchanging looks and smiles and occasionally words. They didn't notice instantly when the sky turned dark, however it didn't take long.  
  
"Captain Janeway to Tuvok."  
  
"Tuvok here," Tuvok's disembodied voice came over the combadge.  
  
"Have the away team regroup, we're getting out of her" she yelled as the plasma storm began to rage. She ended the transmission and began another, "Janeway to Voyager"  
  
"Voyager here, Captain." It was Harry. "What's happening down there. We're getting some strange readings."  
  
"It's a plasma storm, begin beaming up the members of the away team."  
  
"Under stood, captain. We'll do our best but there is a good chance that the storm is going to cause interference with the transports.  
  
"Do your best, Janeway out."  
  
Janeway and Chakotay began looking for the rest of the away team, wanting to insure that they all successfully made it back to the ship. They came over a slight rise and saw them, one by one dematerializing. As the Captain felt the familiar tingle of the transporter beam she glances over and saw that Chakotay was beginning to dematerialize also her mind felt at ease.  
  
Chakotay materialized on the transporter pad, alone. "Where is she!" he shouted at the transporter chief.  
  
"The storm is interfering with the beam out. Her pattern is breaking up." The transporter chief explained, working the console feverishly. "I'm going to try using a second beam to stabilize her pattern." After a few moments he said, "Its working the pattern is stabilizing… wait a moment I'm showing two patterns.  
  
"What?"  
  
"I don't know what happened."  
  
Chakotay pulled a phaser and aimed it at the transporter pad, "well, lets see what we have." Two figures began to materialize on the pad, "Step a way Captain." he warned. Both figures almost jumped away from the other. It took a moment for everyone in the transporter room to register what they were seeing. Upon the transporter pad stood two Kathryn Janeways.  
  
*  
  
The senior staff had assembled in the briefing room; the two Janeways sat at the head of the table.  
  
"There is still no sure explanation for what happened." Chakotay said as he paced the briefing room, "And as far as we can tell there is no way to reverse it. So now we need to figure out what to do about this.  
  
"Well, I suppose we can't have two different captains," Tom quipped trying to ease some of the tension in the room.  
  
"No," he said stopping and placing his hands palm down on the table. "The doctor is working to determine which is the original and which it the duplicate. The original will continue as the captain and the duplicate will choose whatever position on the ship they want."  
  
"EMH to Commander Chakotay."  
  
"Chakotay here."  
  
"I have determined which is the original."  
  
Chakotay glanced quickly to the two identical women next to him, "We'll be right there."  
  
*  
  
"After running several different analyses," the doctor began once they had convened in sickbay, "I have discovered a 0.0012% genetic drift in the captain on you're right."  
  
"Well, I guess that settles that," Chakotay said tuning to the women, "now I'll leave you to discuss things, to decide what happens now." Chakotay left and the Doctor, takeing the hint, deactivated him self."  
  
"I'll pick another name, I think maybe I'll go with our middle name, Elizabeth…"  
  
"No," the captain interrupted her, "no one calls me Kathryn anyway, you can keep the name, I'll take Elizabeth."  
  
"Chakotay calls us Kathryn."  
  
"Well that's only one person."  
  
"Are you sure?"  
  
"Yes."  
  
"If you insist." Kathryn said.  
  
After a pause the captain asked, "So what are you going to do now?"  
  
"Well, with your permission, I think I'd like to work in the science department. It will take a while to get use to taking orders again, but I missed being a scientist."  
  
"Permission granted." The captain said giving her double a slight smile, she was taking this whole thing better than she had expected. She thought since they had been the same person that she should know how Kathryn was thinking but apparently she was wrong. 


	3. Chapter Two

The Captain and Kathryn: Chapter Two  
  
Kathryn was a little nervous as she approached the mess hall the next day. Of course the whole crew had been informed of the happenings of the previous day but hearing and seeing are two different very different things. She paused for a moment to straighten her uniform and brush off the science blue shoulders. Then she stepped forward and allowed the automatic doors to slide open. She spotted Chakotay sitting with Tom B'Elanna and Harry at a table in the corner. She grabbed a tray and moved to join them, ignoring the uncomfortable glances that she was getting from the other crewmembers.  
  
"Good morning, Kathryn." Chakotay said when he saw her.  
  
"Good morning, Chakotay, Tom, B'Elanna, Harry," she greeted each of them.  
  
"Good morning Kathryn," Tom and B'Elanna greeted her in unison taking the cue form Chakotay.  
  
"Good morning, Um…" Harry floundered.  
  
"Kathryn, Harry, my name is Kathryn." She said laughing as she sat down in an empty chair next to Chakotay.  
  
"Yeah Har, you can say it. Kath-ryn." Tom teased Harry, breaking down the name as if teaching it to a toddler. Harry blushed beet red.  
  
"Am I interrupting anything?" All the occupants of the table looked up to see the Captain.  
  
"Of course not, Captain, we're just giving Harry a hard time." B'Elanna said with a smile.  
  
"Have a seat, Captain, there's always room for one more." Tom said gesturing to the one remaining open chair between him and Chakotay.  
  
"I might just take you up on that offer," she said sitting down.  
  
If any of the table's occupants felt uncomfortable with the situation they didn't show it. They all chatted easily over breakfast as if there was nothing unusual about the day. Tom made some joke about how with two Janeways, the Borg didn't stand a chance and the Captain pretended not to notice when Kathryn placed her hand over Chakotay's and left it there. After a while they all left to begin their duty shifts.  
  
~  
  
Captain Janeway didn't see very much of Commander Chakotay that day and that evening she went to have dinner at the messhall in hopes that she would find him there. He wasn't there but instead of eating by her self she took up Tom and Harry's offer for companionship, something that she rarely did, however after how well things had gone that morning she decided that maybe she should spend a little more time socializing with the crew. When Tom mentioned that they were running the Sandrien's program that night she decided that she should stop by.  
  
~  
  
"Captain!" the holographic Sandrien exclaimed when Captain Janeway stepped onto the holodeck a couple of hours later. "Its good to see you. Why didn't you tell me you have a twin?  
  
"A twin?"  
  
"Yes, Kathryn." Sandrien pointed to the pool table where Kathryn was standing next to Chakotay. When the captain didn't say anything Sandrien added, "If she's as good at pool as you are the men around here don't stand a chance"  
  
The captain still didn't say anything, she was watching Kathryn and Chakotay. Even from that distance it was obvious that they were flirting mercilessly. Chakotay was bent over the pool table to make his shot when Kathryn gave him a swift swat on the behind. He dropped his cue, spun on his heal and grabbed Kathryn around her waist to prevent her from getting away form him. As he held her in place he tickled her. The captain was beginning to think that coming to Sandrien's was a bad idea and was about to leave when he spotted her. He almost dropped Kathryn, "Captain! I didn't expect to see you here."  
  
"Its all right Commander, I was just leaving."  
  
"Captain, don't leave yet, you just got here." Tom said approaching her from across the room, "the maintenance overhaul you ordered has B'Elanna stuck in engineering late the least you can do is have a drink with me."  
  
Janeways's eyes were still locked with Chakotay's as she agreed with Tom, she was going to need a drink.  
  
The Captain sat down at the table and took a sip of the drink that Tom handed her. "How strong is this?" she inquired.  
  
"Probably not strong enough, Captain."  
  
"Tom, I need a friend right now, not a helmsman. Call me Elizabeth, at least for tonight."  
  
"OK, Elizabeth," he stumbled slightly over the name, then he chuckled as another thought crossed his mind, "if it was Harry sitting here instead of me, would you have asked him to call you that?"  
  
She smiled, "I don't know, if I did do you think he would?"  
  
Tom laughed out right, "Probably not, he's still calling Kathryn, 'Um…'"  
  
At the mention of the name 'Kathryn' the Captain sighed, "I suppose with the way they've been acting its probably obvious now how I feel about him."  
  
"No, offense, Cap… Elizabeth, but it was obvious before."  
  
The captain sighed once again as she looked back to the pool table. Chakotay had his arm around Kathryn's waist as they watched Harry take his shot. "You're right Tom, this wasn't nearly strong enough," she said and then took one last swig of her drink.  
  
~  
  
Kathryn and Chakotay made their way down the corridors on the way from the holodeck. Kathryn intertwined her fingers with his and reviled in just being close to him. She already missed being the captain but she was now able to be with the man she loved and that pro easily outweighed any cons. They stopped and she realized that they were standing in front of Chakotay's door.  
  
"Well I guess this I goodnight."  
  
"Not so fast," Kathryn said playfully as she pushed him up against a bulkhead and curled her arm around his neck, "Do you know how long I have been in love with you?"  
  
"Probably not as long as I have been in love with you." He whispered  
  
"I wouldn't be so sure," she said then pulled his head down into a long lingering kiss.  
  
"So do you want to come in?" he asked when they had finally pulled apart  
  
"I thought you'd never ask."  
  
As Chakotay lead Kathryn into his quarters neither of the noticed the captain who had come around the corner a few minutes earlier and had witnessed the entire exchange.  
  
To be continued… 


	4. Chapter Three

The Captain and Kathryn: Chapter Three  
  
"Captain's Log: Supplemental  
  
It has been three months since the transporter accident that created my duplicate, Kathryn. She has adjusted well to her roll as my science officer and her performance has been exemplary. The crew has also adjusted well to her…"  
  
Captain Janeway's train of thought was interrupted by the sound of female laughter drifting through the wall that separated her quarters from Chakotay's.  
  
"…presence. Computer: end log." The captain stood and began to pace the room, these walls are suppose to be sound proof," she muttered, trying to concentrate on the report that she held in her hand. Once again Kathryn's laughter penetrated the wall and her newly found concentration was broken again. She sighed and dropped her report onto her desk. She moved over to the replicater. "Coffee, black." She ordered. When the computer complied, she took a sip of the dark liquid and came to the decision that she wasn't going to get any work done as long as she was in her quarters. She gathered her PADDs and, taking her coffee with her, headed to the messhall.  
  
*  
  
"Did you hear anything?" Chakotay asked.  
  
"No."  
  
"I thought I heard the captain's door."  
  
Kathryn shrugged her shoulders slightly and smiled at the man she loved who shifted uneasily on the couch next to her,. "Chakotay are you all right?"  
  
For a moment he didn't say anything, he just looked at the wall that separated his quarters from the captain's. "Yes. No. I guess I'm felling a little guilty."  
  
"Oh Chakotay," she said placing her hand on his forearm,  
  
"It's just that for the past few months I've practically been ignoring her. I'm her best friend, but I'm afraid I haven't been a very good one lately."  
  
"I know her, Chakotay. I know she misses you but that she wants you to be happy, even if it's not with her. I know that she doesn't want you to feel guilty, she feels guilty enough for the both of you."  
  
"Why?"  
  
"For pushing you away all these years."  
  
Chakotay thought on this for a few moments, "are you sure?"  
  
"I'm positive, she will be happy for us. Let's tell her!"  
  
"What, now?"  
  
"Yes, now." Kathryn said, standing and tugging on Chakotay's arm.  
  
"But she's not in her quarters now," he said, chuckling.  
  
"How do you know?"  
  
"I heard her doors, she left."  
  
"You know us too well," she said shaking her head, "I'm going the check just incase. Computer: where is Captain Janeway.  
  
"Captain Janeway is in the Messhall."  
  
"Hmm… you were right."  
  
"Well we can tell her tomorrow, in her ready room."  
  
"That depends, who do you want to tell first our captain or our friend?"  
  
"Our friend," he smiled.  
  
"Then we'll tell her tonight. Computer: notify us when Captain Janeway reenters her quarters."  
  
*  
  
"Elizabeth?"  
  
"What are you doing her Tom?"  
  
"Looking for you, I needed to give you this report and the computer said you were in the messhall, so, here I am." He sat down hard on the couch next to her and handed her his PADD.  
  
She looked at it for a moment and then said, "not that I'm suspicious of you motives or anything, Tom, but this could have waited until morning."  
  
"OK, so I'm checking up on you. What are you doing here?"  
  
"I had to get out of my quarters, she was in Chakotay's with him."  
  
"I see…"  
  
"I'm losing him, Tom. We never have dinner together anymore, he hasn't called me anything but 'Captain' since it happened. I hardly ever see him off duty anymore and when I do, he's with her. I lost him, Tom." She paused for a moment and turned away form Tom, as, against her will, tears were forming in her eyes. "And the horribly ironic thing is that … I lost him to myself, to the me that … he wanted me to be … to the me that I had the potential to be … to the me…"  
  
"To the you that you couldn't be. He knows that, he would have waited for you."  
  
She laughed bitterly, "Yeah, well now he doesn't have to, he has her."  
  
Tom wanted to take her in to his arms and tell her that everything would be all right, but he knew he couldn't. Although she was his friend, she was still the captain, so instead he placed a comforting hand on her shoulder and sat with her in the dark of the abandon messhall.  
  
*  
  
When the Captain finally returned to her quarters, she collapsed on the couch, with every intention of sleeping there, still in her uniform, she really didn't care. It was only a moment before her door chimed. She sighed deeply, sat up and smoothed out her uniform.  
  
"Come in." she tried to think of who it would be. It could be Tom, stopping by to make sure that she didn't do what she had been about to do, or it could be… "Chakotay, Kathryn, how are you this evening." She said putting on her diplomatic captain's smile.  
  
"We're fine, Elizabeth. We have something we want to tell you." Kathryn said giving the captain a genuine smile.  
  
"Have a seat," the Captain said, motioning to the couch, as she sat down in the adjacent chair.  
  
Chakotay looked a little nervous as he sat down next to Kathryn and put his arm around her, "Captain," he began, taking a deep breath, "Kathryn and I would like to get married."  
  
To be continued… 


	5. Chapter Four

A/N: I know it's been along time since I updated this, but I finally got the inspiration to finish it. I should have the rest of it done soon, but here is a short chapter to tide you over.  
  
"Come." Chakotay didn't even look up as he responded to the door chime.  
  
"What the hell are you doing!" The enraged voice of Tom Paris could be heard even before the doors had full opened.  
  
The commander looked up in surprise, "Excuse me?"  
  
"You're marrying her?"  
  
Chakotay sighed as he set down his PADD. He and Kathryn had not yet officially announced their engagement but apparently the rumors were already making their rounds. He had assumed that someone on the ship would have a problem with their relationship but he had expected that person to be the captain not the helmsman. "And you have a problem with this because."  
  
"What about the captain"  
  
Chakotay shifted uncomfortably on his couch and fixed his gaze on the ground. With a voice carefully devoid of emotion he asked, "What about her?"  
  
"How could you do this to her. How could you hurt her like this, your suppose to be her friend." Tom was pacing the length of Chakotay's quarters.  
  
"Tom."  
  
But the agitated lieutenant wouldn't listen, "How could you? You're slime, you're."  
  
Tom let out a string of insults that swirled and ran together in Chakotay's mind until he couldn't tell one from the other. Under any other circumstances he would have thrown Tom in the brig or threatened to bust him down to crewman, but at the moment he felt that he deserved every one of those insults. Even so he tried to defend himself "I love Kathryn and she loves me."  
  
"But you don't love that captain?"  
  
Tom's words stopped Chakotay's dead. He struggle to continue, "I. she. that doesn't matter anymore."  
  
Tom stopped suddenly in front of Chakotay, "That's where you're wrong, it does matter and if you can't see that, then you must be blind."  
  
Chakotay slouched suddenly and began to talk softly as if he was talking to himself, "Kathryn , said that the Captain would be happy for us, that she would want me to be happy."  
  
"and she does, but you can't keep going on as if you don't feel any thing for her and that she doesn't feel anything for you. Even after all that has happened, you're still her best friend. You have to talk to her about this." He paused, waiting for Chakotay to acknowledge this but he didn't.  
  
Chakotay made the promise, but it was a promise that he didn't keep. He wanted to, he tried to. He lost count of the number of times that found himself standing outside the captain's quarters or her ready room, with every intention of going in and having that talk with her. But every time he lost his nerve. 


End file.
